De novo transcriptome assembly provides insight into the specific genes of the carotenoid biosynthetic pathway of Citrullus colocynthis (L.)

Background and Aim: Carotenoids as a group of secondary metabolites are organic tetraterpenoid pigments that are essential for both plant mechanisms and human's health. RNA sequencing (RNA-Seq) has provided unprecedented insights into the information content of plant genomes and transcriptomes. In this study, we used transcriptome sequencing to identify genes expressed in carotenoid biosynthesis in Citrullus colocynthis medical plant.Methods: In this study, to determine the transcriptome sequences of C. colocynthis fruits we performed Illumina HiSeq۲۵۰۰ platform. After the quality control process using FastQC and Trimmomatic software the high-quality reads were assembled using the Evidential-gene de novo assembly program. The sequences of the assembled unigenes were loaded in parallel on different databases including KAAS, Uniprot, etc.Results: The transcriptome sequencing of C. colocynthis fruit resulted in ۲۲,۲۵۵,۲۰۰ raw readings were evaluated qualitatively by removing poor quality reads using relevant software. After the process of quality control, a total of ۲۱,۹۵۲,۸۸۵ high-quality reads were obtained, and ۵۵,۳۱۱ unigenes were obtained by de novo assembly by Evidential-gene software. ۱۳,۶۵۷ unigenes were annotated and mapped into ۱۳۴ pathways by searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Also, ۳,۹۳۵ unigenes have been assigned to specific metabolic pathways, and all of the known enzymes involved in terpenoid backbones biosynthetic and carotenoid biosynthetic pathways were also identified in our library. By examining unigenes related to the biosynthetic pathway of the brassinosteroid hormone, ۶۲ gene KEGG identifiers (K) were identified in ۱۹ pathways. This study has revealed putative cis-phytoene synthase (crtB), ۱۵-cis-phytoene desaturase (PDS/crtP), zeta-carotene isomerase (Z-ISO), zeta-carotene desaturase (ZDS/crtQ) and lycopene epsilon-cyclase (LCYE/crtL۲) might be key factors for carotenoid contents.Conclusion: This report is the first to identify genes associated with carotenoid biosynthesis in C. colocynthis medical plant which has been analyzed through different biosynthetic pathways of this plant. In order to expedite the process of gene discovery, we have undertaken Illumina HiSeq۲۵۰۰ sequencing of RNA prepared from C. colocynthis fruit. Identification of biosynthetic pathways of secondary metabolites in various medicinal plants constitutes a targeted genomic resource for research applications and production of biological and biotechnological products.